RetrogeneDB ID: retro_cjac_1422

Retrocopy location

• Organism: Marmoset (Callithrix jacchus)
• Coordinates: 15:83243380..83244797(-)
• Located in intron of: ENSCJAG00000019203

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: DUS1L
• Ensembl ID: ENSCJAG00000018104
• Aliases: None
• Description: None

Sequence

>retro_cjac_1422
ATGCCAAAGCTGCAGGACTTTGAGTTCTGGAGTCACACCCTTCCGGGGGCCCGCCACGTGGTGGCCCCCATGGTGGACCA
GAGTGAGCTGGCCTGAAGGCTGCTGAGCCGGCGCCAAGGGGCACAGCTCTGCTACACGCCCATGCTACACGCCCAAGTCT
TTGTCCGTGACGCCAGCTACCGGAAGGAGAACCTGTACTGCGAGGTGTGCCTCGAGGACCAGCCCCTCATCGTGCAGTTC
TGTGCCAATGACCCGGAGGTGTTTGTTCAGGTGGCTCTCCTGGTTCAGGGTTACTGTGACGCCATCGACATGAACCCGGG
CTGCCCACAGATGATAGCCAAGAGAGGTCACTATGGCGCCTTCCTGCAGGATGAGTGGGACCTGCTCCAAAGAATGATTT
TGCTGGCCCACGAGAAACTCTCTGTTCCCGTCCCATGCAAAATCCTTGTCTTCCCAGAGATTGACAAGACTGTGAGGTAT
GCCCAGATGCTGGAGAAGGCCGGCTGCCAGTTGCTGATCGTTCATGGGTGCACCAAGCAGCAGAAGGTGCCCCTGTCCAG
TGCAGCATCCTGGGAGCACATTAAGGCTGTGCAGAAAGCTGTGGCCATCCCTGTGTTTGCCAGTGGGAACATCCAGAGCC
TACAGGATGTGTAGCGCTGCATCCAGGACACGGGTGTACAGAGTGTCATGAGTGCAGAAGGCAACCTGCACAACCCTGCC
CTGTTTGAGGGCCGGAGCCCTGCCGTGTGGGAGCTGGCGGAGGATTACCTGGATATCGTGCGGGAGCACCCCTGCCCGCT
GTCCTACGTCCAGGCCCATCTCTTCAAGCTGTGGCACCACACGCTGCGGGTGCATCAGCAGCTGCGAGAGGAGCTGGCCA
AGGTGAAGACCCTGGAGGGCATTGCCGCCGTGAGCCAGGAGCTGAGGATGCGGTGGCAGGAGATATCCAGGCCGGAGGGA
GCAAAGCCCACTGGCGATTTGCCCTTCCACTGGATCTGCCACCCCTATGTCCAGCTGGCGCCCAGGGAGGGGAGCAAGGA
GAAGGCAGGTGCGCGCAGCAAGCAGGCCCTGGAGGAGAAGGAGTGTGGCATGGAAGTCCTGTCCAAGAATAAGCAGAAGA
AGCAGGTGAGGAACCCCCCACGAGACCTTCGACCTCTCTCTGAAGCCAAAATATGCAAAGTGTGATCAGTGTGGCAACCC
AAAGGACAACAGATGTGTGTTCAGCCTGTGCCGCGGCTGCTGCAAGAGGCGAGCCTCCAAAGAGACCGCGGACTGCCTGG
GTTACCGATCGCTTTTTAAAACCAAATTGGAGAAGTCTTTGGCCAGGAAGGAGACCCAGCCTGAGCTGCAGGAGCCTCAG
ACGGCCACACCTGGCACACCAGATGGCTTCTCAGAAGTCATGAGTAGTGCTCTGGCC

Alignment

ORF - retro_cjac_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.26 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPKLQGFEFWSHTLRGARHVVAPMVDQSELAWRLLSRRHGAQLCYTPMLHAQVFVRDANYRKENLYCEVC
          MPKLQ.FEFWSHTL.GARHVVAPMVDQSELA.RLLSRR.GAQL.........VFVRDA.YRKENLYCEVC
Retrocopy MPKLQDFEFWSHTLPGARHVVAPMVDQSELA*RLLSRRQGAQLXXXXXXXXXVFVRDASYRKENLYCEVC

Parental  PEDRPLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
          .ED.PLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL
Retrocopy LEDQPLIVQFCANDPEVFVQVALLVQGYCDAIDMNPGCPQMIAKRGHYGAFLQDEWDLLQRMILLAHEKL

Parental  SVPVTCKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEHIKAVRKAVAIPVFANGN
          SVPV.CKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEHIKAV.KAVAIPVFA.GN
Retrocopy SVPVPCKILVFPEIDKTVRYAQMLEKAGCQLLIVHGCTKQQKVPLSSAASWEHIKAVQKAVAIPVFASGN

Parental  IQSLQDVERCIQDTGVQGVMSAEGNLHNPALFEGRSPAVWELAEEYLDIVREHPCPLSYVRAHLFKLWHH
          IQSLQDV.RCIQDTGVQ.VMSAEGNLHNPALFEGRSPAVWELAE.YLDIVREHPCPLSYV.AHLFKLWHH
Retrocopy IQSLQDV*RCIQDTGVQSVMSAEGNLHNPALFEGRSPAVWELAEDYLDIVREHPCPLSYVQAHLFKLWHH

Parental  TLQVHQQLREELAKVKTLEGIAAVSQELKMRCQEEISRQEGAKPTGNLPFHWICQPYVRPGPRERSKEKA
          TL.VHQQLREELAKVKTLEGIAAVSQEL.MR.Q.EISR.EGAKPTG.LPFHWIC.PYV...PRE.SKEKA
Retrocopy TLRVHQQLREELAKVKTLEGIAAVSQELRMRWQ-EISRPEGAKPTGDLPFHWICHPYVQLAPREGSKEKA

Parental  GARSKRALEEEEECGTEVLSKNKQKKQLRN-PHKTFDPSLKPKYAKCDQCGNPKGNRCVFSLCRGCCKRR
          GARSK.AL.EE.ECG.EVLSKNKQKKQ.RN.PH.TFD.SLKPKYAKCDQCGNPK.NRCVFSLCRGCCKRR
Retrocopy GARSKQAL-EEKECGMEVLSKNKQKKQVRN>PHETFDLSLKPKYAKCDQCGNPKDNRCVFSLCRGCCKRR

Parental  ASKETADCPGHGLLFKTKLEKSLIWKGTQPELQEPQTATPGTPGGFSEVMSSALA
          ASKETADC.G...LFKTKLEKSL..K.TQPELQEPQTATPGTP.GFSEVMSSALA
Retrocopy ASKETADCLGYRSLFKTKLEKSLARKETQPELQEPQTATPGTPDGFSEVMSSALA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP051959_colon	0.35 RPM	12.31 RPM
SRP051959_heart	0.07 RPM	10.26 RPM
SRP051959_kidney	0.07 RPM	15.29 RPM
SRP051959_liver	0.04 RPM	24.11 RPM
SRP051959_lung	0.44 RPM	11.26 RPM
SRP051959_lymph_node	0.64 RPM	12.15 RPM
SRP051959_skeletal_muscle	0.00 RPM	30.97 RPM
SRP051959_spleen	0.61 RPM	12.16 RPM

ChIP-Seq

Callithrix jacchus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cjac_1422 retrocopy.

TSS

Callithrix jacchus was not studied using FANTOM5 data.

Lab

retro_cjac_1422 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cjac_1422 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018104	5 retrocopies	retro_cjac_1422 , retro_cjac_1887, retro_cjac_3451, retro_cjac_4002, retro_cjac_4018,
Monodelphis domestica	ENSMODG00000003351	1 retrocopy	retro_mdom_1097,
Pan troglodytes	ENSPTRG00000009790	1 retrocopy	retro_ptro_883,